miga-base 0.3.0.0 → 0.3.0.1

data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim

@@ -0,0 +1 @@
+gi|4558520|gb|AF033819.3|	1	9182

data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec

@@ -0,0 +1,233 @@
+8528	8627	97.03	169	2
+4500	4599	94.00	152	3
+554	653	96.00	161	6
+5564	5663	93.07	147	9
+1542	1641	95.00	158	12
+4743	4842	94.00	152	14
+2565	2664	94.12	154	17
+7723	7822	96.00	161	18
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+7817	7913	96.94	163	23
+8553	8649	96.91	163	25
+214	310	96.91	163	28
+2602	2701	94.12	154	33
+2086	2185	97.00	169	34
+3397	3496	94.00	150	35
+1333	1430	93.94	148	40
+6501	6600	97.03	169	44
+673	772	96.00	163	46
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+316	415	96.00	163	48
+4830	4929	97.00	169	49
+3925	4024	95.00	156	50
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+958	1057	96.00	163	55
+6744	6841	93.94	148	56
+5974	6073	96.04	163	58
+5867	5966	94.06	152	60
+5438	5536	96.97	167	63
+7137	7236	97.03	169	65
+5002	5101	96.04	163	66
+8509	8606	94.90	154	68
+7966	8064	97.98	171	70
+1900	1999	93.14	148	71
+7554	7653	93.07	147	72
+7408	7507	94.06	152	73
+9071	9170	96.00	163	75
+2	85	95.24	134	75
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+7433	7533	93.20	148	110
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+2	67	93.94	99.0	223
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+213	312	94.06	152	284
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+6898	6997	97.03	169	288
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+4306	4404	97.98	172	320
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+31	129	96.00	161	370
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+678	777	94.06	152	393
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+3892	3991	92.00	139	425
+3599	3698	97.00	169	426
+1408	1508	96.04	165	428
+3341	3440	97.00	167	429
+8316	8415	95.00	156	436
+1809	1908	96.00	163	438
+7770	7869	97.00	169	439
+7250	7349	97.00	169	440
+5590	5688	93.94	150	441
+8475	8574	98.02	174	443
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+7237	7336	96.00	161	451
+2461	2559	94.06	152	454
+1168	1267	95.05	158	455
+3083	3178	95.88	156	457
+5129	5228	99.00	180	463
+8590	8684	96.84	159	464
+2677	2776	93.20	148	465
+8332	8431	95.00	156	466
+7692	7791	96.04	163	470
+51	150	95.00	158	471
+1397	1496	98.00	172	472
+42	141	94.00	152	475
+2117	2216	96.00	161	476
+5481	5579	93.94	147	482
+7809	7908	95.00	158	485
+4991	5089	94.00	148	486
+9059	9158	97.00	167	487
+2	73	95.83	115	487
+133	232	95.10	158	488
+6966	7065	95.10	159	490
+6296	6390	96.84	158	492
+4728	4827	97.00	169	495
+4205	4304	96.08	165	498
+6833	6932	98.00	172	499

data/utils/enveomics/Tests/phyla_counts.tsv

@@ -0,0 +1,10 @@
+OTU	Site A	Site B	Site C	Site D
+Actinobacteria	22	1	2	22
+Dehalococcoidia	44	3	2	44
+Fusobacteria	1	4	2	32
+Nitrospirae	32	3	6	1
+Planctomycetes	11	2	1	11
+Proteobacteria	77	25	38	7
+Spirochaetes	4	11	7	3
+Thermotogae	2	11	1	2
+unclassified	1	1	1	1

data/utils/enveomics/Tests/primate_lentivirus.ogs

@@ -0,0 +1,11 @@
+hiv1	hiv2	siv
+lcl|AF033819.3_prot_AAC82593.1_1	lcl|NC_001722.1_prot_NP_056837.1_2	lcl|NC_001549.1_prot_NP_054369.1_2
+lcl|AF033819.3_prot_AAC82598.2_2	lcl|NC_001722.1_prot_NP_663784.1_1	lcl|NC_001549.1_prot_NP_687035.1_1
+lcl|AF033819.3_prot_AAC82594.1_3	lcl|NC_001722.1_prot_NP_056839.1_3	lcl|NC_001549.1_prot_NP_054370.1_3
+lcl|AF033819.3_prot_AAC82595.1_4	lcl|NC_001722.1_prot_NP_056841.1_5	lcl|NC_001549.1_prot_NP_054371.1_4
+lcl|AF033819.3_prot_AAC82591.1_5	lcl|NC_001722.1_prot_NP_056842.1_6	-
+lcl|AF033819.3_prot_AAC82592.1_6	lcl|NC_001722.1_prot_NP_056843.1_7	-
+lcl|AF033819.3_prot_AAD20388.1_7	-	-
+lcl|AF033819.3_prot_AAC82596.1_8	lcl|NC_001722.1_prot_NP_056844.1_8	lcl|NC_001549.1_prot_NP_054372.1_5
+lcl|AF033819.3_prot_AAC82597.1_9	lcl|NC_001722.1_prot_NP_056845.1_9	lcl|NC_001549.1_prot_NP_054373.1_6
+-	lcl|NC_001722.1_prot_NP_056840.1_4	-

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm

@@ -0,0 +1,9 @@
+lcl|AF033819.3_prot_AAC82593.1_1	lcl|AF033819.3_prot_AAC82593.1_1	100.00	500	0	0	1	500	1	500	0.0	1044	500	500
+lcl|AF033819.3_prot_AAC82598.2_2	lcl|AF033819.3_prot_AAC82598.2_2	100.00	1003	0	0	1	1003	1	1003	0.0	2062	1003	1003
+lcl|AF033819.3_prot_AAC82594.1_3	lcl|AF033819.3_prot_AAC82594.1_3	100.00	192	0	0	1	192	1	192	6e-147	400	192	192
+lcl|AF033819.3_prot_AAC82595.1_4	lcl|AF033819.3_prot_AAC82595.1_4	100.00	78	0	0	1	78	1	78	4e-56	161	78	78
+lcl|AF033819.3_prot_AAC82591.1_5	lcl|AF033819.3_prot_AAC82591.1_5	100.00	86	0	0	1	86	1	86	6e-63	179	86	86
+lcl|AF033819.3_prot_AAC82592.1_6	lcl|AF033819.3_prot_AAC82592.1_6	100.00	116	0	0	1	116	1	116	1e-82	231	116	116
+lcl|AF033819.3_prot_AAD20388.1_7	lcl|AF033819.3_prot_AAD20388.1_7	100.00	82	0	0	1	82	1	82	2e-54	157	82	82
+lcl|AF033819.3_prot_AAC82596.1_8	lcl|AF033819.3_prot_AAC82596.1_8	100.00	856	0	0	1	856	1	856	0.0	1770	856	856
+lcl|AF033819.3_prot_AAC82597.1_9	lcl|AF033819.3_prot_AAC82597.1_9	100.00	123	0	0	1	123	1	123	1e-92	257	123	123

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm

@@ -0,0 +1,8 @@
+lcl|AF033819.3_prot_AAC82593.1_1	lcl|NC_001722.1_prot_NP_056837.1_2	58.19	452	178	7	1	448	1	445	0.0	526	500	521
+lcl|AF033819.3_prot_AAC82598.2_2	lcl|NC_001722.1_prot_NP_663784.1_1	58.24	953	397	1	42	994	498	1449	0.0	1169	1003	1550
+lcl|AF033819.3_prot_AAC82594.1_3	lcl|NC_001722.1_prot_NP_056839.1_3	33.75	160	91	6	2	153	4	156	2e-20	75.9	192	215
+lcl|AF033819.3_prot_AAC82595.1_4	lcl|NC_001722.1_prot_NP_056841.1_5	40.79	76	45	0	2	77	7	82	1e-18	65.9	78	87
+lcl|AF033819.3_prot_AAC82591.1_5	lcl|NC_001722.1_prot_NP_056842.1_6	67.74	31	9	1	18	47	46	76	9e-12	47.8	86	130
+lcl|AF033819.3_prot_AAC82592.1_6	lcl|NC_001722.1_prot_NP_056843.1_7	46.43	28	14	1	8	34	5	32	0.004	25.0	116	103
+lcl|AF033819.3_prot_AAC82596.1_8	lcl|NC_001722.1_prot_NP_056844.1_8	34.47	879	492	22	25	856	19	860	3e-146	447	856	860
+lcl|AF033819.3_prot_AAC82597.1_9	lcl|NC_001722.1_prot_NP_056845.1_9	56.90	58	25	0	66	123	98	155	2e-22	80.1	123	257

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm

@@ -0,0 +1,6 @@
+lcl|AF033819.3_prot_AAC82593.1_1	lcl|NC_001549.1_prot_NP_054369.1_2	52.67	524	208	9	1	496	1	512	0.0	518	500	513
+lcl|AF033819.3_prot_AAC82598.2_2	lcl|NC_001549.1_prot_NP_687035.1_1	60.25	966	373	6	36	994	487	1448	0.0	1196	1003	1472
+lcl|AF033819.3_prot_AAC82594.1_3	lcl|NC_001549.1_prot_NP_054370.1_3	38.71	155	87	7	2	152	4	154	1e-25	90.9	192	219
+lcl|AF033819.3_prot_AAC82595.1_4	lcl|NC_001549.1_prot_NP_054371.1_4	30.43	69	40	3	11	73	21	87	4e-07	34.3	78	118
+lcl|AF033819.3_prot_AAC82596.1_8	lcl|NC_001549.1_prot_NP_054372.1_5	36.16	874	464	26	34	855	22	853	5e-154	467	856	854
+lcl|AF033819.3_prot_AAC82597.1_9	lcl|NC_001549.1_prot_NP_054373.1_6	60.34	58	23	0	66	123	82	139	5e-21	75.9	123	223

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm

@@ -0,0 +1,9 @@
+lcl|NC_001722.1_prot_NP_663784.1_1	lcl|NC_001722.1_prot_NP_663784.1_1	100.00	1550	0	0	1	1550	1	1550	0.0	3210	1550	1550
+lcl|NC_001722.1_prot_NP_056837.1_2	lcl|NC_001722.1_prot_NP_056837.1_2	100.00	521	0	0	1	521	1	521	0.0	1077	521	521
+lcl|NC_001722.1_prot_NP_056839.1_3	lcl|NC_001722.1_prot_NP_056839.1_3	100.00	215	0	0	1	215	1	215	5e-164	446	215	215
+lcl|NC_001722.1_prot_NP_056840.1_4	lcl|NC_001722.1_prot_NP_056840.1_4	100.00	113	0	0	1	113	1	113	6e-85	237	113	113
+lcl|NC_001722.1_prot_NP_056841.1_5	lcl|NC_001722.1_prot_NP_056841.1_5	100.00	87	0	0	1	87	1	87	5e-63	179	87	87
+lcl|NC_001722.1_prot_NP_056842.1_6	lcl|NC_001722.1_prot_NP_056842.1_6	100.00	130	0	0	1	130	1	130	4e-94	262	130	130
+lcl|NC_001722.1_prot_NP_056843.1_7	lcl|NC_001722.1_prot_NP_056843.1_7	100.00	103	0	0	1	103	1	103	2e-72	204	103	103
+lcl|NC_001722.1_prot_NP_056844.1_8	lcl|NC_001722.1_prot_NP_056844.1_8	100.00	860	0	0	1	860	1	860	0.0	1799	860	860
+lcl|NC_001722.1_prot_NP_056845.1_9	lcl|NC_001722.1_prot_NP_056845.1_9	100.00	257	0	0	1	257	1	257	0.0	536	257	257

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm

@@ -0,0 +1,6 @@
+lcl|NC_001722.1_prot_NP_663784.1_1	lcl|NC_001549.1_prot_NP_687035.1_1	56.99	1474	601	10	1	1458	1	1457	0.0	1697	1550	1472
+lcl|NC_001722.1_prot_NP_056837.1_2	lcl|NC_001549.1_prot_NP_054369.1_2	57.39	528	203	7	1	521	1	513	0.0	593	521	513
+lcl|NC_001722.1_prot_NP_056839.1_3	lcl|NC_001549.1_prot_NP_054370.1_3	44.97	169	88	5	1	167	1	166	6e-41	132	215	219
+lcl|NC_001722.1_prot_NP_056841.1_5	lcl|NC_001549.1_prot_NP_054371.1_4	35.21	71	42	2	17	83	22	92	3e-11	46.2	87	118
+lcl|NC_001722.1_prot_NP_056844.1_8	lcl|NC_001549.1_prot_NP_054372.1_5	44.90	873	401	14	25	859	23	853	0.0	714	860	854
+lcl|NC_001722.1_prot_NP_056845.1_9	lcl|NC_001549.1_prot_NP_054373.1_6	41.74	230	108	5	1	224	1	210	2e-50	158	257	223

data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm

@@ -0,0 +1,6 @@
+lcl|NC_001549.1_prot_NP_687035.1_1	lcl|NC_001549.1_prot_NP_687035.1_1	100.00	1472	0	0	1	1472	1	1472	0.0	3045	1472	1472
+lcl|NC_001549.1_prot_NP_054369.1_2	lcl|NC_001549.1_prot_NP_054369.1_2	100.00	513	0	0	1	513	1	513	0.0	1067	513	513
+lcl|NC_001549.1_prot_NP_054370.1_3	lcl|NC_001549.1_prot_NP_054370.1_3	100.00	219	0	0	1	219	1	219	7e-169	459	219	219
+lcl|NC_001549.1_prot_NP_054371.1_4	lcl|NC_001549.1_prot_NP_054371.1_4	100.00	118	0	0	1	118	1	118	3e-87	243	118	118
+lcl|NC_001549.1_prot_NP_054372.1_5	lcl|NC_001549.1_prot_NP_054372.1_5	100.00	854	0	0	1	854	1	854	0.0	1776	854	854
+lcl|NC_001549.1_prot_NP_054373.1_6	lcl|NC_001549.1_prot_NP_054373.1_6	100.00	223	0	0	1	223	1	223	5e-170	462	223	223

data/utils/enveomics/build_enveomics_r.bash

@@ -0,0 +1,44 @@
+#!/bin/bash
+
+cd $(dirname -- $0)/enveomics.R
+rm man/*
+echo '
+\name{phyla.counts}
+\docType{data}
+\alias{phyla.counts}
+\title{Counts of microbial phyla in four sites}
+\description{
+  This data set gives the counts of phyla in three different
+  sites.
+}
+\usage{phyla.counts}
+\format{A data frame with 9 rows (phyla) and 4 rows (sites).}
+\keyword{datasets}
+' > man/phyla.counts.Rd
+echo '
+\name{growth.curves}
+\docType{data}
+\alias{growth.curves}
+\title{Bacterial growth curves for three Escherichia coli mutants}
+\description{
+  This data set provides time (first column) and three triplicated growth
+  curves as optical density at 600nm (OD_600nm) for different mutants of E.
+  coli.
+}
+\usage{growth.curves}
+\format{A data frame with 16 rows (times) and 10 rows (times and OD_600nm).}
+\keyword{datasets}
+' > man/growth.curves.Rd
+echo "
+library(inlinedocs)
+package.skeleton.dx('./');
+" | R --vanilla
+cat man/enveomics.R-package.Rd | tr -d '\r' \
+   | grep -v '^}$' | grep -v '^\\author{' \
+   | grep -v '^Maintainer' \
+   | perl -pe 's/^\\keyword/}\n\\author{Luis M. Rodriguez-R <lmrodriguezr\@gmail.com> [aut, cre]}\n\n\\keyword/' \
+   | perl -lwe '$/=\0; $_=<>; s/^\\details{\n+([^}].*\n+)*}\n+//mg; print' \
+   > o && mv o man/enveomics.R-package.Rd
+#[[ ! -d inst/doc ]] && mkdir -p inst/doc
+#pandoc -o inst/doc/enveomics.R.pdf -f markdown_github README.md
+

data/utils/enveomics/enveomics.R/DESCRIPTION

@@ -0,0 +1,31 @@
+Package: enveomics.R
+Version: 1.1.5
+Authors@R: c(person("Luis M.","Rodriguez-R",role=c("aut","cre"),
+	   email="lmrodriguezr@gmail.com"))
+Title: Various Utilities for Microbial Genomics and Metagenomics
+Description: A collection of functions for microbial ecology and other
+   applications of genomics and metagenomics. Companion package for the
+   Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016
+   <DOI:10.7287/peerj.preprints.1900v1>).
+Author: Luis M. Rodriguez-R [aut, cre]
+Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>
+URL: http://enve-omics.ce.gatech.edu/enveomics
+Depends:
+   R (>= 2.9),
+   stats,
+   methods,
+   parallel,
+   modeest,
+   fitdistrplus,
+   sn,
+   investr
+Suggests:
+   tools,
+   vegan,
+   ape,
+   picante,
+   gplots,
+   optparse
+License: Artistic-2.0
+LazyLoad: yes
+Encoding: UTF-8

data/utils/enveomics/enveomics.R/NAMESPACE

@@ -0,0 +1,35 @@
+import(methods)
+import(modeest)
+import(parallel)
+import(fitdistrplus)
+import(sn)
+importFrom("investr", "predFit")
+importFrom("grDevices", "boxplot.stats", "col2rgb", "grey", "rainbow",
+  "rgb")
+importFrom("graphics", "abline", "axis", "barplot", "hist", "image",
+  "layout", "legend", "lines", "par", "points", "polygon",
+  "rect", "text")
+importFrom("stats", "as.dist", "cophenetic", "cor", "median",
+  "quantile", "runif", "smooth.spline", "nls", "nls.control", "qnorm")
+importFrom("utils", "head", "read.table", "setTxtProgressBar", "tail",
+  "txtProgressBar")
+exportClasses(enve.RecPlot2, enve.RecPlot2.Peak, enve.TRIBS, enve.TRIBStest,
+  enve.GrowthCurve)
+S3method(plot, enve.RecPlot2)
+S3method(plot, enve.TRIBS)
+S3method(plot, enve.TRIBStest)
+S3method(plot, enve.GrowthCurve)
+S3method(summary, enve.TRIBS)
+S3method(summary, enve.TRIBStest)
+S3method(summary, enve.GrowthCurve)
+export(
+  enve.cliopts, enve.col.alpha,
+  enve.barplot, enve.recplot, enve.prune.dist,
+  enve.tribs, plot.enve.TRIBS, summary.enve.TRIBS, enve.tribs.test,
+  plot.enve.TRIBStest, summary.enve.TRIBStest,
+  enve.df2dist, enve.df2dist.group, enve.df2dist.list,
+  enve.recplot2, plot.enve.RecPlot2, enve.recplot2.findPeaks,
+  enve.recplot2.corePeak, enve.recplot2.changeCutoff,
+  enve.recplot2.extractWindows,
+  enve.growthcurve, plot.enve.GrowthCurve, summary.enve.GrowthCurve,
+  enve.col2alpha)

data/utils/enveomics/enveomics.R/R/autoprune.R

@@ -0,0 +1,121 @@
+
+enve.prune.dist <- function
+### Automatically prunes a tree, to keep representatives of each clade.
+   (t,
+### A `phylo` object or a path to the Newick file.
+   dist.quantile=0.25,
+### The quantile of edge lengths.
+   min_dist,
+### The minimum distance to allow between two tips. If not set, dist.quantile is
+### used instead to calculate it.
+   quiet=FALSE,
+### Boolean indicating if the function must run without output.
+   max_iters=100,
+### Maximum number of iterations.
+   min_nodes_random=4e4,
+### Minimum number of nodes to trigger "tip-pairs" nodes sampling. This sampling
+### is less reproducible and more computationally expensive, but it's the only
+### solution if the cophenetic matrix exceeds 2^31-1 entries; above that, it
+### cannot be represented in R.
+   random_nodes_frx=1
+### Fraction of the nodes to be sampled if more than `min_nodes_random`.
+   ){
+   if(!requireNamespace("ape", quietly=TRUE))
+      stop('Unavailable ape library.');
+   if(is.character(t)) t <- ape::read.tree(t)
+   if(missing(min_dist)){
+      if(dist.quantile>0){
+	 min_dist <- as.numeric(quantile(t$edge.length, dist.quantile));
+      }else{
+         min_dist <- as.numeric(min(t$edge.length[t$edge.length>0]));
+      }
+   }
+   if(!quiet) cat('\nObjective minimum distance: ',min_dist,', initial tips: ',length(t$tip.label),'\n', sep='');
+   round=1;
+   while(round <= max_iters){
+      if(length(t$tip.label) > min_nodes_random){
+	 if(!quiet) cat('  | Iter: ',round-1,', Tips: ', length(t$tip.label),
+	 	', reducing tip-pairs.\n', sep='');
+         rnd.nodes <- sample(t$tip.label, length(t$tip.label)*random_nodes_frx);
+	 t <- enve.__prune.reduce(t, rnd.nodes, min_dist, quiet);
+      }else{
+	 if(!quiet) cat(' Gathering distances...\r');
+	 d <- cophenetic(t);
+	 diag(d) <- NA;
+	 if(!quiet) cat('  | Iter: ',round-1,', Tips: ', length(t$tip.label),
+		', Median distance: ', median(d, na.rm=TRUE),
+      		', Minimum distance: ', min(d, na.rm=TRUE),
+		'\n', sep='');
+	 # Run iteration
+	 if(min(d, na.rm=TRUE) < min_dist){
+	    t <- enve.__prune.iter(t, d, min_dist, quiet);
+	 }else{
+	    break;
+	 }
+      }
+      round <- round + 1;
+   }
+   return(t);
+### Returns a pruned phylo object.
+}
+
+enve.__prune.reduce <- function
+### Internal function for enve.prune.dist
+   (t, nodes, min_dist, quiet){
+   if(!quiet) pb <- txtProgressBar(1, length(nodes), style=3);
+   for(i in 1:length(nodes)){
+      node.name <- nodes[i];
+      if(!quiet) setTxtProgressBar(pb, i);
+      # Get node ID
+      node <- which(t$tip.label==node.name);
+      if(length(node)==0) next;
+      # Get parent and distance to parent
+      parent.node <- t$edge[ t$edge[,2]==node, 1];
+      # Get edges to parent
+      parent.edges <- which(t$edge[,1]==parent.node);
+      stopit <- FALSE;
+      for(j in parent.edges){
+	 for(k in parent.edges){
+	    if(j != k & t$edge[j,2]<length(t$tip.label) & t$edge[k,2]<length(t$tip.label) & sum(t$edge.length[c(j,k)]) < min_dist){
+	       t <- ape::drop.tip(t, t$edge[k,2]);
+	       stopit <- TRUE;
+	       break;
+	    }
+	 }
+	 if(stopit) break;
+      }
+   }
+   if(!quiet) cat('\n');
+   return(t);
+}
+
+enve.__prune.iter <- function
+### Internal function for enve.prune.dist
+   (t,
+   dist,
+   min_dist,
+   quiet){
+   ori_len <- length(t$tip.label);
+   # Prune
+   if(!quiet) pb <- txtProgressBar(1, ncol(dist)-1, style=3);
+   ignore <- c();
+   for(i in 1:(ncol(dist)-1)){
+      if(i %in% ignore) next;
+      for(j in (i+1):nrow(dist)){
+	 if(dist[j, i]<min_dist){
+	    t <- ape::drop.tip(t, rownames(dist)[j]);
+	    ignore <- c(ignore, j);
+	    break;
+	 }
+      }
+      if(!quiet) setTxtProgressBar(pb, i);
+   }
+   if(!quiet) cat('\n');
+   # Check if it droped tips
+   cur_len <- length(t$tip.label);
+   if(cur_len == ori_len){
+      stop("Internal error: small edge found in tree, with no equivalent in distance matrix.\n");
+   }
+   return(t);
+}
+